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Question: makeTranscriptDbFromUCSC() error
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gravatar for Chris Cabanski
3.8 years ago by
Chris Cabanski30 wrote:
Hi, I am encountering an error when running makeTranscriptDbFromUCSC() that was not occurring yesterday. I have tried on 2 separate computers/R versions and get similar errors. Playing around, it seems like the function works for other genomes but not for hg19, which is what I am looking for. Any ideas on what is going wrong? > library("TxDb.Hsapiens.UCSC.hg19.knownGene") > tx <- makeTranscriptDbFromUCSC(genome="hg19",tablename="refGene") Error in tableNames(ucscTableQuery(session, track = track)) : error in evaluating the argument 'object' in selecting a method for function 'tableNames': Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 2 elements > traceback() 2: tableNames(ucscTableQuery(session, track = track)) 1: makeTranscriptDbFromUCSC(genome = "hg19", tablename = "refGene") > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1 [2] GenomicFeatures_1.14.2 [3] AnnotationDbi_1.24.0 [4] Biobase_2.22.0 [5] GenomicRanges_1.14.4 [6] XVector_0.2.0 [7] IRanges_1.20.6 [8] BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] biomaRt_2.18.0 Biostrings_2.30.1 bitops_1.0-6 BSgenome_1.30.0 [5] DBI_0.2-7 RCurl_1.95-4.1 Rsamtools_1.14.2 RSQLite_0.11.4 [9] rtracklayer_1.22.0 stats4_3.0.2 tools_3.0.2 XML_3.98-1.1 [13] zlibbioc_1.8.0 -- Christopher Cabanski, PhD Postdoctoral Research Associate Department of Medicine, Oncology Division / The Genome Institute Washington University in St. Louis https://www.sites.google.com/site/crcabanski/ ____ This email message is a private communication. The information transmitted, including attachments, is intended only for the person or entity to which it is addressed and may contain confidential, privileged, and/or proprietary material. Any review, duplication, retransmission, distribution, or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is unauthorized by the sender and is prohibited. If you have received this message in error, please contact the sender immediately by return email and delete the original message from all computer systems. Thank you.
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Chris Cabanski30
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gravatar for Chris Cabanski
3.8 years ago by
Chris Cabanski30 wrote:
You can disregard my previous message. makeTranscriptDbFromUCSC() is working correctly again. -Chris > Hi, > I am encountering an error when running makeTranscriptDbFromUCSC() that > was not occurring yesterday. I have tried on 2 separate computers/R > versions and get similar errors. Playing around, it seems like the > function works for other genomes but not for hg19, which is what I am > looking for. Any ideas on what is going wrong? > >> library("TxDb.Hsapiens.UCSC.hg19.knownGene") > >> tx <- makeTranscriptDbFromUCSC(genome="hg19",tablename="refGene") > Error in tableNames(ucscTableQuery(session, track = track)) : > error in evaluating the argument 'object' in selecting a method for > function 'tableNames': Error in scan(file, what, nmax, sep, dec, quote, > skip, nlines, na.strings, : > line 1 did not have 2 elements > >> traceback() > 2: tableNames(ucscTableQuery(session, track = track)) > 1: makeTranscriptDbFromUCSC(genome = "hg19", tablename = "refGene") > >> sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1 > [2] GenomicFeatures_1.14.2 > [3] AnnotationDbi_1.24.0 > [4] Biobase_2.22.0 > [5] GenomicRanges_1.14.4 > [6] XVector_0.2.0 > [7] IRanges_1.20.6 > [8] BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] biomaRt_2.18.0 Biostrings_2.30.1 bitops_1.0-6 > BSgenome_1.30.0 > [5] DBI_0.2-7 RCurl_1.95-4.1 Rsamtools_1.14.2 > RSQLite_0.11.4 > [9] rtracklayer_1.22.0 stats4_3.0.2 tools_3.0.2 XML_3.98-1.1 > [13] zlibbioc_1.8.0 > > ____ This email message is a private communication. The information transmitted, including attachments, is intended only for the person or entity to which it is addressed and may contain confidential, privileged, and/or proprietary material. Any review, duplication, retransmission, distribution, or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is unauthorized by the sender and is prohibited. If you have received this message in error, please contact the sender immediately by return email and delete the original message from all computer systems. Thank you.
ADD COMMENTlink written 3.8 years ago by Chris Cabanski30
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